How to generate FPKM values for Velvet/Oases assembled transcripts

Question

[upendrakumar.devisetty]

Hi,

Can anyone point to me of how i can generate FPKM values for the Velvet/Oases assembled transcripts. I know TopHat/Cufflinks pipeline for generating FPKM values but in this case i already have Velvet/Oases assembled transcripts along with the reads. All i want to do is to see the expression levels of Velvet/Oases assembled transcripts. Any help is appreciated.

[Ram]

So you don't have reads, or you have reads as well as transcripts?

[upendrakumar.devisetty]

I have both reads and transcripts

[Ram]

Thank you for the clarification - I've modified your question to reflect this.

[upendrakumar.devisetty]

Thanks for the modification. Appreciated

[poisonAlien]

I think you can still use your transcripts (in gtf format) with cufflinks to measure expression. Just provide transcripts file as reference annotation.

 -G/--GTF                     quantitate against reference transcript annotations

[upendrakumar.devisetty]

Good point. I have the transcripts in bed format and probably can change them to gtf and use them but how about the bam file (accepted_hits.bam) file that is need as input with cufflinks ? Do you think i should map all the reads from which i generated transcripts from using TopHat and then run cufflinks? Please advise

[poisonAlien]

No need to align again. Just us the same bam file which was used to generate the tx annotation file.